Always expanding light to 3-component was considered but rejected because it would create a dependency on having coloured light support in an engine before BSP2 could be implemented. An extra optional lump is a possibility (we didn't reserve space in the header for marking this kind of thing though

) but I'm not seeing how it's much different from just having a LIT file too.
LIT files are nice. You can delete them, move them around, recompile your lighting without affecting the source BSP, keep multiple copies for experimenting with, etc. All advantages. I can see that including it in the BSP can make distribution easier, but in this case I think the case for not including outweighs.